Biology subjects

Smith, I.

Publications and source records attributed to Smith, I..

At least 19 recordsLinked to original sources

bioRxiv2026

Extracellular matrix defects destabilise apical cytoarchitecture and mechanical properties during early Down syndrome neurodevelopment

Down syndrome (DS) is associated with altered brain development, especially in the cerebellum. However, how trisomy 21 (TS21) is linked to cerebellar defects remains poorly understood. Cerebellar organoids reveal that TS21 leads to extracellular matrix (ECM) alterations, perturbing downstream pathways linked to reduction of apical RAB11+ endosomes. These changes lead to impaired apical maintenance and altered progenitor composition. Significantly, ECM-enriched culture rescues apical defects in TS21 organoids, supporting a functional role for ECM in preserving apical organisation and progenitor niche integrity. In the developing human DS cerebellum and 2D neural cultures, where exogenous ECM is present, severe epithelial disorganisation is attenuated. Nevertheless, ECM organisation and mechanical properties remain altered in 2D cultures. Our findings identify TS21-driven ECM abnormalities as a mechanism impairing apical integrity, progenitor composition and mechanical proprieties in neural stem cell models of DS. Altogether, we established apical maintenance instability as an early developmental defect contributing for DS neuropathology.

Developmental Biology↗

bioRxiv2026

Acute priming using elevated fluid viscosity recovers young-like single-cellsurveillance behaviors in aged human T cells

Aging is a complex biological process, often characterized by increased vulnerability to disease, infection, and death. This increased vulnerability is mechanistically linked to a progressive and functional decline of the immune system. In humans, aged lymphocytes lose their capacity to effectively surveil within diverse microenvironments, decreasing their capability for clearing infections and maintaining physiological homeostasis. However, specific mechanisms by which aged lymphocytes, specifically T cells, lose this capacity to surveil remain unclear. We profiled three core characteristics of T cell surveillance at single-cell resolution, specifically migration, deformability, and sensing. While aged T cells retained their capacity for spontaneous migration, they exhibited impaired cellular deformability and deficiencies in sensing local signaling cues. To modulate this surveillance defect, we performed mechanical reprogramming using elevated fluid viscosity. Results showed that acute priming of aged T cells with elevated fluid viscosity recovered a transient young-like surveillance phenotype, which was mechanistically linked to membrane tension, cortical F-actin, and Arp3 expression. These findings reveal a key source of surveillance defects in aged T cells and provide an effective mechanical approach to tuning their single-cell behaviors. TeaserRecovery of young-like surveillance phenotypes in aging human T cells via viscosity priming

bioengineering↗

bioRxiv2025

Asymmetric leading vs. trailing edge shifts since the Last Glacial Maximum underpin the modern bimodal latitudinal diversity gradient in planktonic foraminifera

AimThe modern latitudinal diversity gradient of planktonic foraminifera is bimodal with a distinct depression near the equator, surrounded by mid-latitude diversity peaks. This pattern emerged after the Last Glacial Maximum, but it is unclear how species spatial dynamics contributed to its formation. Here, we investigate how species range dynamics, i.e., trailing-edge contractions (extirpations) and leading-edge expansions (colonisations), shaped the modern bimodal pattern, and how global biodiversity patterns arise from local patterns. LocationGlobal open ocean, with basin-specific analyses in the Atlantic and Pacific Oceans. Time periodLast Glacial Maximum (19 - 23 ka) (LGM) and the Pre-Industrial (modern) Major taxa studiedPlanktonic foraminifera (unicellular eukaryotes) MethodsWe analysed taxonomically standardized LGM and modern foraminiferal assemblage datasets to characterize changes in species richness at multiple spatial scales: global ocean, basin-wide, and within basin. We quantified species range shifts by comparing their trailing- and leading-edge movements. We estimated temporal turnover locally, and the net imbalance between colonisations and extirpations (NICE) within sites, and tested whether species thermal preferences correlate with their extirpation risk. ResultsWe found no evidence of systematic trailing edge contractions, indicating that equatorial extirpations did not drive the bimodal LDG pattern. In the Atlantic, leading-edge expansions generated a coherent increase in species richness in the mid-latitudes, whereas the Pacific exhibited highly spatially heterogeneous responses, including extirpation hotspots in the western tropical Pacific and colonisation zones in the eastern and southern Pacific. Species thermal optima weakly predicted extirpations, with species adapted to lower temperatures more at risk of extirpation, consistent with the general warming trend since the last ice age. Main conclusionsThe modern bimodal LDG of planktonic foraminifera arises primarily from mid-latitude colonisations rather than equatorial extirpations. Colonisations were particularly frequent in the North Atlantic. Localized extirpations in the western Pacific highlight small-scale patches of vulnerability, that spatially aggregated richness metrics mask. Our results underscore the need to distinguish between trailing and leading processes in climate-induced range shifts, and to consider spatial variability in monitoring and protection of marine biodiversity.

ecology↗

bioRxiv2025

Releasing RNA from formalin: novel 20th century rotavirus alphagastroenteritidis strains identified in Australian microbat voucher specimens

Archival specimens held in biorepositories (e.g. natural history collections) offer rare temporal snapshots of global biodiversity. These collections not only preserve species morphology and aspects of ecology, but increasingly provide access to historical molecular data, including insights into wildlife disease. As several pandemics have originated from animal viruses spilling over into the human population (i.e., SARS-CoV-2/COVID-19, 2009 H1N1 influenza, and HIV/AIDS), characterising the diversity of viruses circulating in wildlife populations is essential for proactive pandemic preparedness. Yet, current surveillance remains biased toward contemporary viruses of economic importance. One solution to bridging spatiotemporal gaps in wildlife virus knowledge is retrospective screening of vouchered wildlife specimens. However, such efforts have been hindered by formalin fixation of specimens, which degrades and cross-links nucleic acids. Here we demonstrate that formalin-fixed vouchered wildlife specimens retain both host and viral RNA fragments after being stored for up to sixty years. We recovered fragments of divergent strains of Rotavirus alphagastroenteritidis from two Australian microbat species; Nyctophilus geoffroyi (lesser long-eared bat) and Rhinolophus megaphyllus (smaller horseshoe bat), representing the first characterisation of Rotavirus alphagastroenteritidis in Australian bats, and the oldest identification of the virus to date. Concurrently, we sequenced endogenous host RNA, providing a proof-of- concept for dual host-virus transcript recovery from vouchered specimens. This study highlights the role biorepositories can play in reconstructing historical viral landscapes and enabling spatiotemporal host-virus insight to advance both biodiversity science and global pandemic preparedness.

genomics↗

bioRxiv2025

Perfusion Bioreactor Culture Incorporating Mechanical Confinement Enhances Mesenchymal Stem Cell Extracellular Vesicle Production and Wound Healing Potential

Mesenchymal stem cell extracellular vesicles (MSC EVs) have been widely studied for regenerative medicine and tissue repair applications. However, clinical translation of EV therapeutics has been hampered by low potency and lack of scalable production strategies. This work aims to develop a novel approach that exploits the mechanosensitivity of MSCs to enhance EV potency in the context of enhanced production via bioreactor culture. MSCs are well known to respond to mechanical stimuli such as substrate stiffness and shear stress, and here it is shown that exposing MSCs to another mechanoregulatory parameter, confinement, enhances the pro-angiogenic bioactivity of their EVs. This is consistent across both donor-derived primary MSCs and induced pluripotent stem cell-derived MSCs (iMSCs). The development of a 3D-printed perfusion bioreactor system that enables culture of confined MSCs under flow is also detailed here, resulting in a 67-fold increase in EV production compared to flask culture. iMSC EVs obtained downstream of this confinement-bioreactor culture induce greater vascularization and generally improve wound healing in a diabetic mouse model compared to iMSC EVs from conventional tissue culture. Overall, this work establishes the development of a scalable, bioreactor-based iMSC EV production platform that provides a solution to major translational bottlenecks of therapeutic EVs.

bioengineering↗

bioRxiv2025

Inhibition of interferon signalling improves rabbit calicivirus replication in biliary organoid cultures

The Rabbit haemorrhagic disease virus (RHDV) was discovered 40 years ago. This highly pathogenic virus threatens the integrity of ecosystems in the European rabbits native range, while in Australia, it is used as a biocontrol tool to manage overabundant populations of feral rabbits (Oryctolagus cuniculus). Little is known about the life cycle of this virus due to the absence of a reliable cell culture system. In 2023, we developed a rabbit liver-derived organoid cell culture system that supports RHDV replication but is unable to sustain serial passaging in culture. Here, we report that the interferon signalling pathway inhibitor Ruxolitinib increases virus replication in organoid-derived monolayer cells and, for the first time, enables the serial passaging of RHDV in cell culture. Four consecutive passages were achieved with viral titres reaching the concentration of the initial virus stock as measured by RT-qPCR. Immunofluorescence analysis showed that more cells are infected in the presence of Ruxolitinib. Furthermore, we noted that cells grew faster and formed healthier monolayers in the presence of the interferon inhibitor. To determine the cellular composition of the monolayers, we used single-cell RNA-sequencing, revealing that our organoids consist largely of RHDV-permissive cholangiocytes. IMPORTANCEIn this work, we describe the use of interferon inhibitor to enhance the permissiveness of our recently developed rabbit liver-derived organoid cell culture to RHDV infection. Interferon inhibitors offer a simple and cost-effective approach to increase the replication of difficult-to-grow viruses in culture systems that are not interferon-deficient.

microbiology↗

bioRxiv2025

Genetic risk in endolysosomal network genes correlates with endolysosomal dysfunction across neural cell types in Alzheimer's disease

Late-onset Alzheimer disease (LOAD) has a complex genomic architecture. LOAD risk variants suggest multiple pathways, including the endolysosomal network (ELN), contribute to the pathobiology of Alzheimer disease (AD). Whether genetic risk in specific pathways correlates with corresponding biological dysfunction remains largely unknown. We developed an endolysosomal pathway-specific polygenic risk score (ePRS) using 14 well-established AD risk alleles implicating ELN genes. We investigated the association between ePRS and AD neuropathology, then examined cell-specific endolysosomal morphology and transcriptomic profiles in post-mortem dorsolateral prefrontal cortex samples from donors stratified by ePRS burden. We found that the ePRS was significantly associated with AD diagnosis and neuropathological measures, comparable to a pathway-agnostic PRS despite representing far fewer loci. High ePRS correlated with increased neuronal endosome volume, number and perinuclear aggregation independent of AD pathology. Single-nucleus RNA sequencing revealed cell type-specific transcriptomic changes associated with ePRS status, influencing glutamatergic signaling, protein homeostasis, responses to DNA damage and immune function. Neurons, astrocytes, oligodendrocytes, and microglia each showed varied gene expression patterns associated with ePRS burden. Together, these results provide evidence that AD genetic risk variants harboring ELN genes correlate with endolysosomal dysfunction in human brain tissue. These findings suggest that pathway-specific genetic risk contributes to corresponding cellular pathology in AD and nominates candidate mechanisms by which ELN AD variants contribute to pathogenesis.

neuroscience↗

bioRxiv2025

A standardized, open-source, portable model for noninvasive joint injury in mice

Preclinical models of osteoarthritis (OA) are crucial for the study of disease mechanisms and for the development of critically-needed disease-modifying therapeutics. While surgical OA models, such as the destabilization of the medial meniscus (DMM), have been the gold standard in the field for decades, noninvasive joint loading-based models have increased in popularity and utility. To facilitate standardization of the noninvasive anterior cruciate ligament rupture (ACLR) model in mice, we present the Mobile Joint-Injury Operator (MoJO) - an open-source protocol with accompanying fixtures and data, designed for a low-cost, commercially-available, portable uniaxial testing system with a small footprint. We provide 3d-printable fixture designs and a rapid, highly-repeatable ACLR-mediated joint injury protocol that results in the expected post-traumatic osteoarthritis phenotype in male and female C56Bl/6 mice. We then describe the expected mechanical data from the injury procedure and offer various troubleshooting strategies. Finally, we summarize the resultant PTOA phenotype by knee hyperalgesia testing, {micro}CT imaging, flow cytometry, and histological assessment. Increased standardization of this model is a critical aspect of the overall refinement of animal models of OA.

physiology↗

bioRxiv2024

Towards a Taxonomy Machine. A Training Set of 5.6 Million Arthropod Images

The taxonomic identification of organisms from images is an active research area within the machine learning community. Current algorithms are very effective for object recognition and discrimination, but they require extensive training datasets to generate reliable assignments. This study releases 5.6 million images with representatives from 10 arthropod classes and 26 insect orders. All images were taken using a Keyence VHX-7000 Digital Microscope system with an automatic stage to permit high-resolution (4K) microphotography. Providing phenotypic data for 324,000 species derived from 48 countries, this release represents, by far, the largest dataset of standardized arthropod images. As such, this dataset is well suited for testing the efficacy of machine learning algorithms for identifying specimens to higher taxonomic categories.

bioinformatics↗

bioRxiv2024

ER and SOCE Ca2+ signals are not required for directed cell migration in human microglia

The central nervous system (CNS) is constantly surveilled by microglia, highly motile and dynamic cells deputed to act as the first line of immune defense in the brain and spinal cord. Alterations in the homeostasis of the CNS are detected by microglia that respond by migrating toward the affected area. Understanding the mechanisms controlling directed cell migration of microglia is crucial to dissect their responses to neuroinflammation and injury. We used a combination of pharmacological and genetic approaches to explore the involvement of calcium (Ca2+) signaling in the directed migration of induced pluripotent stem cell (iPSC)-derived microglia challenged with a purinergic stimulus. This approach mimics cues originating from injury of the CNS. Unexpectedly, simultaneous imaging of microglia migration and intracellular Ca2+ changes revealed that this phenomenon does not require Ca2+ signals generated from the endoplasmic reticulum (ER) and store-operated Ca2+ entry (SOCE) pathways. Instead, we find evidence that human microglial chemotaxis to purinergic signals is mediated by cyclic AMP in a Ca2+-independent manner. These results challenge prevailing notions, with important implications in neurological conditions characterized by perturbation in Ca2+ homeostasis.

neuroscience↗

bioRxiv2023

Ribose lowers RpoS translation through RbsD mRNA

The Escherichia coli sigma factor RpoS accumulates during starvation, activates transcription of the general stress response, and then rapidly returns to low levels upon nutrient replenishment. Sugar levels modulate RpoS levels by signaling though central metabolism, ATP and the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS) transport system, which favors glucose. However, there have been few examples of dedicated control pathways for specific sugars regulating RpoS. We screened an overexpression library with a RpoS- LacZ reporter and found that overexpressing the ribose metabolism rbsD gene reduced RpoS levels. A functional RbsD ribose pyranase protein was not necessary for the effect, suggesting that the RbsD mRNA was responsible for the effect. We used a series of LacZ fusions and RT-qPCR to determine how RbsD mRNA affects RpoS and found that regulation of RpoS occurred at the level of translation. Furthermore, the effect of rbsD overexpression was diminished in strain that did not have the RpoS untranslated hairpin loop or the small RNA chaperone Hfq. RbsD mRNA has previously been shown to bind to the sRNA DsrA. We demonstrated that the effect of RbsD on RpoS was dependent on the sRNAs DsrA and ArcZ and Hfq. Finally, we showed that the sugar ribose lowers RpoS levels in a manner that requires RbsD. In summary, our results demonstrate that RpoS levels respond specifically to ribose though a component of the ribose metabolism pathway and the main player, RbsD, acts as dual function mRNA that has a regulatory role by interacting with the sRNAs that control RpoS.

genetics↗

bioRxiv2023

Similarity metric learning on perturbational datasets improves functional identification of perturbations

Analysis of high-throughput perturbational datasets, including the Next Generation Connectivity Map (L1000) and the Cell Painting projects, uses similarity metrics to identify perturbations or disease states that induce similar changes in the biological feature space. Similarities among perturbations are then used to identify drug mechanisms of action, to nominate therapeutics for a particular disease, and to construct bio-logical networks among perturbations and genes. Standard similarity metrics include correlations, cosine distance and gene set enrichment methods, but these methods operate on the measured features without refinement by transforming the measurement space. We introduce Perturbational Metric Learning (PeML), a weakly supervised similarity metric learning method to learn a data-driven similarity function that maximizes discrimination of replicate signatures by transforming the biological measurements into an intrinsic, dataset-specific basis. The learned similarity functions show substantial improvement for recovering known biological relationships, like mechanism of action identification. In addition to capturing a more meaningful notion of similarity, data in the transformed basis can be used for other analysis tasks, such as classification and clustering. Similarity metric learning is a powerful tool for the analysis of large biological datasets.

bioinformatics↗

bioRxiv2023

Eating an elephant, one bite at a time: predator interactions at carrion bonanzas

Resource specific competition between predators has typically been studied from their interactions at meso-herbivore carcasses, because such carcasses are abundant. Mega-carcasses like those of elephants are rare but unparalleled in the extent of carrion biomass they offer and the long durations they can persist. These rare resource bonanzas can thus provide unique opportunities to understand sympatric species interactions within likely relaxed competitive scenarios. Using remote cameras that were operational 24-h a day, we monitored two elephant carcasses in Tsavo, Kenya, from when they were discovered until they were completely consumed or became inaccessible. While we found high temporal overlaps in activity patterns between all predators, the terrestrial predator guild (lion/leopard/spotted hyena) was not observed to feed simultaneously, suggesting strong interference competition. Based on photo-analysis and video-evidence of exclusion from a carcass, interference competition within the terrestrial predator guild favored lions over hyenas, and hyenas over leopards. The carcass at the terrestrial-aquatic interface showed more simultaneous feeding bouts between predators (crocodile/spotted hyena), indicating either facilitation and/or higher coexistence between predators that typically occupy different niches. We also observed a hippopotamus scavenging from an elephant carcass, thereby documenting a rare instance of a megaherbivore feeding on a megaherbivore. Our results highlight the importance of monitoring such carcasses through remote cameras, which can significantly add to our existing understanding of food webs and carrion ecology.

ecology↗

bioRxiv2023

Detection of circular RNAs and their potential as biomarkers predictive of drug response

The introduction of high-throughput sequencing technologies has allowed for comprehensive RNA species detection, both coding and non-coding, which opened new avenues for the discovery of predictive and prognostic biomarkers. However the consistency of the detection of different RNA species depends on the RNA selection protocol used for RNA-sequencing. While preliminary reports indicated that non-coding RNAs, in particular circular RNAs, constitute a rich source of biomarkers predictive of drug response, the reproducibility of this novel class of biomarkers has not been rigorously investigated. To address this issue, we assessed the inter- lab consistency of circular RNA expression in cell lines profiled in large pharmacogenomic datasets. We found that circular RNA expression quantified from rRNA-depleted RNA-seq data is stable and yields robust prognostic markers in cancer. On the other hand, quantification of the expression of circular RNA from poly(A)-selected RNA-seq data yields highly inconsistent results, calling into question results from previous studies reporting their potential as predictive biomarkers in cancer. We have also identified median expression of transcripts and transcript length as potential factors influencing the consistency of RNA detection. Our study provides a framework to quantitatively assess the stability of coding and non-coding RNA expression through the analysis of biological replicates within and across independent studies.

bioinformatics↗

bioRxiv2022

Meta-analysis of preclinical pharmacogenomic studies to discover robust and translatable biomarkers of drug response

Preclinical pharmacogenomic studies provide an opportunity to discover novel biomarkers for drug response. However, pharamcogenomic studies linking gene expression profiles to drug response do not always agree on the significance or strength of biomarkers. We apply a statistical meta-analysis approach to 7 large independent pharmacogenomic studies, testing for tissue-specific gene expression markers predictive of response among cancer cell lines. We found 4,338 statistically-significant biomarkers across 8 tissue types and 34 drugs. Significant biomarkers were found to be closer than random to drug targets in a gene network built on pathway co-membership (average distance of 2 vs 2.9). However, functional relationships with the drug target did not predict reproducibility across studies. To validate these biomarkers, we utilized 10 clinical datasets, allowing 42/4338 biomarkers to be assessed for clinical translation. Of the 42 candidate biomarkers, the expression of ODC1 was found to be significantly predictive of Paclitaxel response as a neoadjuvant treatment of breast carcinoma across 2 independent clinical studies of >200 patients each. We expect that as more clinical transcriptomics data matched with response are available, our results can be used to prioritize which genes to evaluate as clinical biomarkers of drug response.

cancer biology↗

bioRxiv2022

Similarity bias from averaging signatures from the Connectivity Map

In recent years, high-throughput perturbational datasets have become an important tool for rapidly characterizing the function of large collections of chemical compounds. To overcome the biological and technical noise in these experiments, researchers have used consensus signatures - averages of multiple experiments - to summarize the effects of perturbations. In this work, we demonstrate that consensus signatures on the L1000 Connectivity Map show a pervasive similarity bias: as more signatures are averaged, the resulting consensus signatures are increasingly similar to each other, regardless of whether the signatures are related. We show that the distribution of Pearsons correlation changes as a function of the number of signatures averaged. The artifactual similarity bias is caused by skewness in the data and a consequence of using median normalization on non-normal distributions. Furthermore, we show that mean normalization can partly remedy this similarity bias and improve power to identify associations. The similarity bias introduced by consensus signatures is an important potential confounder of analysis of perturbational datasets, and our practical solution could easily be applied by practitioners in the field to improve the analysis of the L1000 Connectivity Map.

bioinformatics↗

bioRxiv2021

TREM2 regulates purinergic receptor-mediated calcium signaling and motility in human iPSC-derived microglia

The membrane protein TREM2 (Triggering Receptor Expressed on Myeloid cells 2) regulates key microglial functions including phagocytosis and chemotaxis. Loss-of-function variants of TREM2 are associated with increased risk of Alzheimers disease (AD). Because abnormalities in Ca2+ signaling have been observed in several AD models, we investigated TREM2 regulation of Ca2+ signaling in human induced pluripotent stem cell-derived microglia (iPSC-microglia) with genetic deletion of TREM2. We found that iPSC-microglia lacking TREM2 (TREM2 KO) show exaggerated Ca2+ signals in response to purinergic agonists, such as ADP, that shape microglial injury responses. This ADP hypersensitivity, driven by increased expression of P2Y12 and P2Y13 receptors, results in greater release of Ca2+ from the endoplasmic reticulum (ER) stores, which triggers sustained Ca2+ influx through Orai channels and alters cell motility in TREM2 KO microglia. Using iPSC-microglia expressing the genetically encoded Ca2+ probe, Salsa6f, we found that cytosolic Ca2+ tunes motility to a greater extent in TREM2 KO microglia. Despite showing greater overall displacement, TREM2 KO microglia exhibit reduced directional chemotaxis along ADP gradients. Accordingly, the chemotactic defect in TREM2 KO microglia was rescued by reducing cytosolic Ca2+ using a P2Y12 receptor antagonist. Our results show that loss of TREM2 confers a defect in microglial Ca2+ response to purinergic signals, suggesting a window of Ca2+ signaling for optimal microglial motility.

neuroscience↗

bioRxiv2021

Novel Hendra virus variant detected by sentinel surveillance of Australian horses.

A novel Hendra virus (HeV) variant, not detected by routine testing, was identified and isolated from a Queensland horse that suffered acute, fatal disease consistent with HeV infection. Whole genome sequencing and phylogenetic analysis demonstrated the variant to have ~83% nucleotide identity to the prototype HeV strain. An updated RT-qPCR assay was designed for routine HeV surveillance. In silico and in vitro comparison of the receptor-binding protein with prototypic HeV showed that the human monoclonal antibody m102.4 used for post-exposure prophylaxis, as well as the current equine vaccine, should be effective against this variant. Genetic similarity of this virus to sequences detected from grey-headed flying-foxes suggests the variant circulates at-least in this species. Studies determining infection kinetics, pathogenicity, reservoir-species associations, viral-host co-evolution and spillover dynamics for this virus are urgently needed. Surveillance and biosecurity practices should be updated to appreciate HeV spillover risk across all regions frequented by flying foxes.

molecular biology↗